In February 2001, BGI received the Advanced Group of 1% of Human Genome Project for the 15th Anniversary of National 863 Program Award granted by the Ministry of Science and Technology, P.R.C.

On January 15, 2002, BGI received the Ccertificate of Top 10 China News of Fundamental Research – Chinese Part of International Human Genome Project issued by Ministry of Science and Technology, P.R.C.

In 2003, BGI received the Illustrious Scientific Achievement Award of Chinese Academy of Science granted by the Chinese Academy of Science.

In 2003, BGI received the Board of Chinese Top 10 China Scientific Achievement 2002 for the detailed map of rice genome.

On March 3, 2003, BGI received the Illustrious Scientific Achievement Award of Chinese Academy of Science – Chinese Hybrid Rice Genome Project granted by the Chinese Academy of Science.

In February 2005, BGI received the Advance Group Medal of Chinese Medical Rescue Team in Indian Ocean Tsunami granted by Chinese Committee of Education, Science, Culture, Health and Sports.

In January 2007, BGI received the Outstanding Product Award of the Fist Chinese Genome Map granted by the 9th China Hi-Tech Fair Committee.

In 2007, BGI received the “Best Exhibition Board Award of 2007 International Conference of Genomics” and “Best Travel Supplement Award of 2007 International Conference of Genomics” in the 2007 International Conference of Genomics.

In September 2008, BGI received the “Honorary Certificate for Medical and Healthcare Support in Beijing 2008 Olympic Games, Beijing 2008 Paralympic Games”, and the “Honorary Certificate of Outstanding Contribution in Beijing 2008 Olympic Games and Medical and Healthcare Support in the 13th Paralympic Games”, granted by Beijing Municipal Health Bureau.

In October 2008, Jun Wang, the executive director of BGI, was selected as “The 100 Most Influential Men” by the 10th China Hi-Tech Fair Committee.

On January, 16, 2009, Wang Jun, the executive director of BGI, was awarded 2008 Thermo Fisher Top-10 Life Scientists.

In June 2009, BGI received The City’s Innovation Award of Technology for the research project of “The Diploid Genome Sequence of an Asian Individual” granted by Shenzhen Government.

On November 17, 2009, BGI received the nomination of Bluesky Award of Global Top Investment Scenarios to Apply New Technologies for Renewable Energy Utilization granted by Shenzhen International Technology Promotion Center for Sustainable Development (ITPC) and United Nations Industrial Development Organization (UNIDO).

On December 25, 2009, Yingrui Li, and Hancheng Zheng received the “New 80s Star of the Year” of the Shenzhen Life Award 2009.

In 2009, BGI won the 1st and 2nd Prizes of Enterprise Group in the “Red Bull Shenzhen - Mountain Sport Challenge Championship 2009” granted by Shenzhen Mountaineering & Outdoor Sport Association

In January 2010, BGI received the Title of “Advance Group 2009 of Shenzhen Science and Technology Association System” granted by Shenzhen Science and Technology Association.

On April 27 2010, Prof. Jun Wang, the executive director of BGI received the Honorary Title of National Model Worker 2010.

In August 2010, BGI received the Certificate of China Red Cross Humanitarian Service Medal granted by china Red Cross.

In September 2010, Jian Wang, the director of BGI received the Environmental Protection Prize of Shenzhen Citizen 2010.

On September 2nd, 2010, Dr. Huanming Yang, the president of BGI received the Certificate of “Innovative People of 30 Worthy People in the 30th Anniversary of Shenzhen Special Economic Zone”.

In December 2010, Reproduction and Cloning, Natural or Artificial, a book written by Dr. Huanming Yang, the president of BGI, won The 2nd Chinese Government Award for Publishing granted by the General Administration of Press and Publication of the People’s Republic of China.

In 2010, Xin Jin and Haojing Shao received the Title of “Guangdong Top 10 Newsmakers 2010”.

In 2010, BGI received the Group Participation Trophy in the Mount Marathon Race of Yantian, Shenzhen 2010.

In 2011, BGI received “The 2010 Top 10 Technology News of China” for the publication of panda genome.

On November 11, 2011, BGI received the Special Award of Merit in the New Year Party 2011 organized by Yantian District Government.

On January 18, 2011, the award ceremony of “2010 CCTV China Economic Person of the Year” was held in Beijing. Jian Wang, the director of BGI was granted the “Innovation Award of 2010 CCTV China Economic Person of the Year”.

On January 20, 2011, Shi Wang, the Chairman of China Vanke Co. Ltd visited BGI and donated skin cells for the research project of induced stem cells. He wrote the inscription “Delivering Love, Storing Hopes, Extending Life” for BGI’s project of stem cell storage.

On January 25, 2011, Chinese Red Cross awarded BGI the Red Cross Medal.

On February 28, 2011, BGI received the honorary certificate of Caring Donation of Floating Population for its donation of providing HPV Genotyping Test to 100,000 floating population.

In March 2011, BGI receive the title of “Shenzhen “March 8” Red Flag Group (2009 – 2010)” granted by Shenzhen Women’s Federation.

On March 16, 2011, Professor Huanming Yang, the President of BGI, received the Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research in Human Genome Meeting 2011(HGM).

On April 20, 2011, Jingkui Yin, the sales director of France of BGI and the working team of HLA typing, received the Title of “Model Worker” and “Advanced Group” of Yantian District 2008 – 2010 respectivitely.

On April 25, 2011, Jun Wang, the executive director of BGI received Individual Award of Guangdong Youth Day (May 4th) Medal.

On April 28,2011, BGI received the “National Labor Award” in the International Labor Day Commendatory Meeting hosted by Shenzhen Labor Party.

In May 2011, BGI Shenzhen, the headquarters of BGI, was ranked 4th of Top 10 Institutions in the Nature Publishing Index (NPI) 2010 China published by Nature Publishing Group.

On June 20, 2011, Lin Fang, the Director of Bioinformatics Centre received the new HPC Innovation Excellence Award at the International Supercomputing Conference(ISC11), granted by International Data Corporation (IDC).

On December 12, 2011,BGI was honored with the Research Partnership Award by the International Research Institute for the Semi-Arid Tropics (ICRISAT) in its 39th anniversary celebration.

On April 25, 2012, Bio-IT World magazine announced the winners of its eighth Best Practices Awards program. BGI was honored with the award for their flexible green cloud computing infrastructure for de novo assembly and re-sequencing analysis.

On June 18, 2012, International Data Corporation (IDC) announced the new winners of the HPC Innovation Excellence Award at the 2012 International Supercomputing Conference (ISC'12) in Hamburg, Germany. BGI, for the second time, was honored with the award for their great achievements and strong return on investment (ROI) by applying high performance computing (HPC) technologies.

On September 5, 2012, Professor Huanming Yang, Academician of Chinese Academy of Sciences and Chairman of BGI, was recently elected as a member of the German National Academy of Sciences, due to his outstanding contributions to the field of Human Genomics and Genetics.

On December 20, 2012Nature announced Ten People Who Mattered This Year.Thirty-six-year-old BGI Executive Director Jun Wang is on the list and also the only Chinese.

On February 17, 2013, BGI has been ranked 4th of Fast Company’s 2013 The World's Top 10 Most Innovative Companies in China for advancing both the science and the business of genetic sequencing.

On February 20, 2013, BGI has been identified in the field of biomedicine as one of 2013’s 50 Disruptive Companies, MIT Technology Review’s annual list of the world’s most innovative technology companies.

In March of 2013, Nature Publishing Group published Nature Publishing Index (NPI) 2012 Asia Pacific. BGI Shenzhen is ranked 6th of China Top 10 Institutions and 18th of Asia Pacific Top 200 Institutions. 

On May 30, 2013, Nature Publishing Group published Nature Publishing Index 2012 China which covers the calendar year 2012. BGI was ranked 6th of 2012 Top 10 Institutions and 5th of Top 10 Institutions over the past five years.

On June 5, 2013, Thomson Reuters announced this year's Hottest Researchers and Research. Jun Wang, Director of BGI, was named one of the Hottest Scientific Researchers.

On June 20, 2013, Nature Publishing Group released Nature Publishing Index 2012 Global. BGI was ranked 119 of Global Top 200 Scientific Institutions in 2012.

On September 19, 2013FORTUNE reveals its annual 40 Under 40 list of the hottest young stars in business. BGI’s 37-year-old director Jun Wang ranked No. 8 on the list, becoming the first Chinese scientist ever to be listed and the first in Biotechnology field.

On October 1, 2013, researchers from BGI were presented with this year’s BioMed Central Open Data Award for their work demonstrating that DNA methylation occurs in the parasitic worm Trichinella spiralis, a human pathogen.

On February 10, 2014, Fast Company announced 2014 ranking of The World's 50 Most Innovative Companies and the Top 10 Most Innovative Companies in 10 critical areas. BGI has been ranked No. 37 in the top 50 and for the second time listed in the Top 10 in China.

On March 27, 2014, Nature Publishing Group released Nature Publishing Index (NPI) 2013 Asia-Pacific. BGI was ranked 5th of 2013 Top 10 Chinese Institutions, up from last year’s 6th. In the Asia-Pacific Top 200 list, BGI raised one place to 17th.

On June 18, 2014, Huanming Yang, Jian Wang, Jun Wang and Yingrui Li were listed as Thomson Reuters’ Highly Cited Researchers.  

On October 6, 2014, Jun Wang, Director of BGI, was listed on CNBC NEXT LIST in Genomics for the next 25 years.

On November 14, 2014, The World Technology Network announced The 2014 World Technology Award winners. BGI was the winner in the corporate category of biotechnology.

On December 17, 2014, Nature presented Nature Index 2014 China. BGI was ranked 5th of Top institutions in Nature and Science, 15th of Top institutions: Life sciences and 48th of Top 200 institutions in the 68 natural science journals that comprise the Nature Index.

On November 12, 2015, Nature Publishing Group today released the Nature Index 2015 Collaborations Supplement. BGI ranks the top of industrial organizations by collaboration score. 

On December 17, 2015, Nature Publishing Group today published the Nature Index 2015 China Supplement. BGI ranks 3rd of Top Institutions in Nature and Science

On March 30, 2016, Huanming Yang and Jian Wang from BGI were named Thomson Reuters Highly Cited Researchers in the field of Molecular Biology & Genetics.

On April 20, 2016, Nature announced Nature Index 2016 Tables. BGI ranks tops of Chinese corporate institutions and 12th of global corporate institutions.